|Evaluation of comparative protein modeling by MODELLER|
A Sali, L Potterton, F Yuan, H Van Vlijmen, M Karplus
Proteins: Structure, Function, and Genetics 23 (3), 318-326, 1995
|A community effort to assess and improve drug sensitivity prediction algorithms|
JC Costello, LM Heiser, E Georgii, M Gönen, MP Menden, NJ Wang, ...
Nature biotechnology 32 (12), 1202-1212, 2014
|Normal mode analysis: theory and applications to biological and chemical systems|
Q Cui, I Bahar
CRC press, 2005
|Programming goes back to school|
Communications of the ACM 55 (5), 38-40, 2012
|PDB-based protein loop prediction: parameters for selection and methods for optimization|
HWT van Vlijmen, M Karplus
Journal of molecular biology 267 (4), 975-1001, 1997
|Improving the accuracy of protein pKa calculations: conformational averaging versus the average structure|
HWT van Vlijmen, M Schaefer, M Karplus
Proteins: Structure, Function, and Bioinformatics 33 (2), 145-158, 1998
|A community computational challenge to predict the activity of pairs of compounds|
M Bansal, J Yang, C Karan, MP Menden, JC Costello, H Tang, G Xiao, ...
Nature biotechnology 32 (12), 1213-1222, 2014
|Affinity enhancement of an in vivo matured therapeutic antibody using structure‐based computational design|
LA Clark, PA Boriack‐Sjodin, J Eldredge, C Fitch, B Friedman, KJM Hanf, ...
Protein science 15 (5), 949-960, 2006
|Proteochemometric modeling as a tool to design selective compounds and for extrapolating to novel targets|
GJP van Westen, JK Wegner, AP IJzerman, HWT van Vlijmen, A Bender
MedChemComm 2 (1), 16-30, 2011
|Identification of a new murine tumor necrosis factor receptor locus that contains two novel murine receptors for tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)|
P Schneider, D Olson, A Tardivel, B Browning, A Lugovskoy, DH Gong, ...
Journal of Biological Chemistry 278 (7), 5444-5454, 2003
|Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set|
EB Lenselink, N Ten Dijke, B Bongers, G Papadatos, HWT Van Vlijmen, ...
Journal of cheminformatics 9 (1), 1-14, 2017
|Trends in antibody sequence changes during the somatic hypermutation process|
LA Clark, S Ganesan, S Papp, HWT van Vlijmen
The Journal of Immunology 177 (1), 333-340, 2006
|Electrostatic contributions to molecular free energies in solution|
M Schaefer, HWT Van Vlijmen, M Karplus
Advances in protein chemistry 51, 1-58, 1998
|Mutations of the anti-mullerian hormone gene in patients with persistent mullerian duct syndrome: biosynthesis, secretion, and processing of the abnormal proteins and analysis …|
C Belville, H Van Vlijmen, C Ehrenfels, B Pepinsky, AR Rezaie, JY Picard, ...
Molecular Endocrinology 18 (3), 708-721, 2004
|The role of polar interactions in the molecular recognition of CD40L with its receptor CD40|
J Singh, E Garber, HV Vlijmen, M Karpusas, YM Hsu, Z Zheng, D Thomas, ...
Protein science 7 (5), 1124-1135, 1998
|Binding of a potent small-molecule inhibitor of six-helix bundle formation requires interactions with both heptad-repeats of the RSV fusion protein|
D Roymans, HL De Bondt, E Arnoult, P Geluykens, T Gevers, ...
Proceedings of the National Academy of Sciences 107 (1), 308-313, 2010
|Novel bicyclic piperazine derivatives of triazolotriazine and triazolopyrimidines as highly potent and selective adenosine A2A receptor antagonists|
H Peng, G Kumaravel, G Yao, L Sha, J Wang, H Van Vlijmen, T Bohnert, ...
Journal of medicinal chemistry 47 (25), 6218-6229, 2004
|Recent advances in chemoinformatics|
DK Agrafiotis, D Bandyopadhyay, JK Wegner, H van Vlijmen
Journal of chemical information and modeling 47 (4), 1279-1293, 2007
|Normal mode calculations of icosahedral viruses with full dihedral flexibility by use of molecular symmetry|
HWT van Vlijmen, M Karplus
Journal of molecular biology 350 (3), 528-542, 2005
|Identification of potent and novel α4β1 antagonists using in silico screening|
J Singh, H van Vlijmen, Y Liao, WC Lee, M Cornebise, M Harris, I Shu, ...
Journal of medicinal chemistry 45 (14), 2988-2993, 2002